LAMMPS (18 Feb 2013)
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 36 45
10 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5 	  	      clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

# 2 chains of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 37 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems

#dump		1 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	1 pad 5

timestep 	0.0001
thermo		50
run		10000
Memory usage per processor = 1.90508 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045743 
     850    17821.483    711.53827            0    3681.7854    7.4384277 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19375            0    3681.3037    11.787983 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184717 
    1150    20849.582    206.01695            0    3680.9472  -0.86699149 
    1200    21815.003    45.317415            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064078 
    1300    20780.781    217.36506            0    3680.8286    6.0538616 
    1350    20558.971    254.36482            0    3680.8601   -3.6773956 
    1400    21485.029    99.812922            0    3680.6511   -16.185473 
    1450    21771.107    52.159608            0    3680.6775   -2.4756674 
    1500    21520.948    93.503928            0    3680.3286    2.1023577 
    1550    21351.418    121.68138            0    3680.2511     5.515995 
    1600    20778.805    216.92177            0    3680.0559    15.089187 
    1650    21477.638    100.21835            0    3679.8247   -1.1045756 
    1700    18501.339    596.47913            0    3680.0357   -15.679677 
    1750    18563.642    587.34787            0    3681.2882    33.532207 
    1800    19110.186    494.82333            0    3679.8543    18.024046 
    1850    21364.191    119.23538            0    3679.9339    2.5291119 
    1900    20146.628    322.14841            0    3679.9197    5.7313081 
    1950    20692.671    231.25336            0    3680.0319    4.2977737 
    2000    20943.904    189.11227            0    3679.7629   -22.645146 
    2050    19668.063    401.82894            0    3679.8394    3.6252006 
    2100    20280.448    299.76054            0    3679.8353    7.4807993 
    2150    19181.869    483.52061            0    3680.4987    22.620257 
    2200     21300.14    130.70883            0    3680.7322     4.710318 
    2250    20486.992    266.63125            0    3681.1299   -8.6453582 
    2300    18653.249    572.22692            0    3681.1018   -5.2639533 
    2350    21513.474    95.623043            0    3681.2021   -9.3615923 
    2400    21466.352    103.55115            0    3681.2765   -29.563489 
    2450     20099.92    332.30226            0    3682.2888     35.75288 
    2500    20764.233    221.69469            0    3682.4003   -12.472324 
    2550    20434.265    276.55013            0     3682.261   -22.406554 
    2600    21466.593    104.51528            0    3682.2808   -10.076416 
    2650    20808.645    214.25423            0    3682.3618    5.1518496 
    2700    18565.645     588.3715            0    3682.6457     22.26312 
    2750    20753.062    223.37556            0    3682.2193   -7.8155982 
    2800    20986.776    184.39985            0    3682.1958   -7.0608776 
    2850    16721.211    895.59298            0    3682.4615    33.619161 
    2900     19294.24    466.43871            0    3682.1454    8.0033435 
    2950     20471.71    270.09532            0     3682.047    2.5545202 
    3000    20609.248    247.27073            0    3682.1453   -1.8817723 
    3050    18576.568    586.31423            0    3682.4089   -1.7806882 
    3100    19790.767    383.54865            0    3682.0099   -6.0384293 
    3150    20941.678    191.88039            0      3682.16    4.7195299 
    3200    20187.734    317.22178            0    3681.8441    7.1381064 
    3250    19982.327    351.80543            0    3682.1932   -10.356822 
    3300    19720.165    395.60482            0     3682.299    12.415019 
    3350    20008.047    347.27468            0    3681.9491    5.0458582 
    3400    20411.522    280.16521            0    3682.0855   -7.1769483 
    3450    20046.145    341.27051            0    3682.2947   0.22584972 
    3500    17937.429     692.9726            0     3682.544    16.131523 
    3550    18771.683    553.86993            0    3682.4837   -1.5944448 
    3600    19901.288    364.81878            0    3681.7001    -24.39551 
    3650    20746.323    224.83374            0    3682.5543   -7.6981313 
    3700    21681.686    68.935986            0    3682.5503   -5.7316854 
    3750    21130.966    160.34639            0     3682.174    2.5404231 
    3800    19573.729    419.87434            0    3682.1625    10.483835 
    3850    19672.797    403.73028            0    3682.5297    7.9092657 
    3900    19429.209    444.39996            0    3682.6014    4.6871663 
    3950    18794.538    550.12554            0    3682.5485   -3.4850598 
    4000    18356.499    622.71257            0    3682.1291    21.961288 
    4050    18499.159     599.5728            0    3682.7659    9.7197804 
    4100    18893.082    533.58148            0    3682.4285    7.1537738 
    4150    18555.438    590.46012            0    3683.0331   -5.9854705 
    4200    20095.772    332.86056            0    3682.1558    6.0048046 
    4250    21395.629    117.09714            0    3683.0352   -12.849296 
    4300    20642.157    242.80387            0    3683.1634   -7.1285142 
    4350    16782.008    886.90013            0    3683.9014    59.279202 
    4400    21722.722    63.477041            0    3683.9307   -6.7708918 
    4450    21483.705    103.77396            0    3684.3914   -14.801558 
    4500    18637.223    577.90593            0    3684.1097    -5.399645 
    4550    21501.072    101.01026            0    3684.5223   -0.2687012 
    4600     21419.25    114.67746            0    3684.5525   -5.1248351 
    4650    19532.212    428.88221            0     3684.251   -13.937733 
    4700    19108.648    500.22789            0    3685.0025   0.72814013 
    4750    21304.939    134.30984            0     3685.133   -10.419682 
    4800    21011.564    183.12003            0    3685.0474  -0.21596054 
    4850    21288.378    137.28914            0    3685.3522    -3.783224 
    4900    20238.761    312.44314            0      3685.57  -0.89650269 
    4950     20973.64     190.4195            0    3686.0262    2.3977528 
    5000    20982.662    188.75492            0    3685.8652   -10.898981 
    5050    20287.196    304.79028            0    3685.9895    7.9988821 
    5100    20161.046    325.98224            0    3686.1566    11.304549 
    5150      20768.1    224.94586            0    3686.2959   -11.679983 
    5200    20550.091    261.40569            0    3686.4209   -3.8503144 
    5250    20274.307    307.08369            0    3686.1349    3.2350203 
    5300    21107.734    168.31547            0    3686.2711   -2.7299125 
    5350    21575.088    90.511714            0    3686.3597   -23.416041 
    5400    19335.208    463.98466            0    3686.5193    1.1686111 
    5450    20334.202    297.13584            0    3686.1696    7.9612042 
    5500    18596.894    586.39323            0    3685.8756     19.42362 
    5550    16402.199    953.72484            0    3687.4247   -7.6804149 
    5600    19716.462    400.17421            0    3686.2512   0.73274328 
    5650    19794.552    387.60203            0     3686.694    7.4829917 
    5700    21404.995    119.38491            0     3686.884    1.1256427 
    5750    21737.498    64.038982            0    3686.9553   0.66497166 
    5800    21196.338    153.70183            0    3686.4248   -4.0562788 
    5850    18817.877    550.28735            0    3686.6001    15.517346 
    5900     20855.92    210.47881            0    3686.4654   -6.7252193 
    5950    18187.477    655.72108            0    3686.9673    -5.840425 
    6000    21574.226    91.415225            0    3687.1196   -4.1947877 
    6050    20647.597    245.36705            0    3686.6333   -4.2710188 
    6100    20195.663    320.68953            0    3686.6333    1.9183471 
    6150    19569.943    425.30544            0    3686.9627   -2.0191803 
    6200    21009.348    185.15969            0    3686.7176   -1.5383241 
    6250    21311.107    135.08699            0    3686.9382   -8.4198399 
    6300    18617.034    583.66046            0    3686.4994    11.716969 
    6350    19818.978    382.62883            0    3685.7919    4.9679172 
    6400    21403.509    119.46416            0    3686.7156   -1.3369474 
    6450    16394.437    955.35248            0    3687.7587    22.900909 
    6500    15570.429    1095.0835            0     3690.155    -24.50813 
    6550    20905.847    202.70205            0    3687.0099   -5.4533991 
    6600    20419.664    282.65592            0    3685.9333   -1.0348411 
    6650    16008.949    1023.4924            0    3691.6506    48.451181 
    6700    18929.104    531.79459            0    3686.6452     8.487112 
    6750     20317.67     301.1228            0    3687.4011   -9.6972866 
    6800    21238.238    147.54216            0    3687.2486    -4.457873 
    6850    19469.334    441.11845            0    3686.0075    29.322933 
    6900    20880.087    207.70983            0    3687.7244   -4.1197403 
    6950    20864.561    210.00891            0    3687.4358   -9.4014401 
    7000    21701.899    70.744638            0    3687.7278    2.6762921 
    7050    18936.455    531.70563            0    3687.7815    29.134314 
    7100    21418.983    118.08942            0    3687.9199   0.64845095 
    7150     21271.75    142.65664            0    3687.9482   -6.1860835 
    7200    21584.017    90.531714            0    3687.8679   -15.915843 
    7250    20478.212    274.65055            0    3687.6858    3.5293379 
    7300    20787.975    223.07914            0    3687.7416    8.3746157 
    7350    21169.849    159.84727            0    3688.1554     4.806229 
    7400    18050.739    679.46766            0    3687.9242    0.1356599 
    7450    21759.344    61.894907            0    3688.4523   -6.0686382 
    7500    20115.323    334.36139            0    3686.9153   -3.9834726 
    7550    21513.687    103.04204            0    3688.6565   -3.6546291 
    7600    20396.612    289.44922            0    3688.8845    8.3149013 
    7650     19954.93    363.06299            0    3688.8846    6.7857536 
    7700    20579.453    259.44475            0    3689.3535   -13.300779 
    7750    21435.784    117.44734            0     3690.078   -3.5454036 
    7800    19676.963    410.82634            0    3690.3202     16.17995 
    7850    22001.763    23.427845            0    3690.3883   -3.2253193 
    7900    21367.244    128.97238            0    3690.1797   -10.139451 
    7950    21835.619    51.102569            0    3690.3723   -6.9113133 
    8000    21081.866    176.87472            0     3690.519    -3.400648 
    8050    17587.847    759.00567            0    3690.3134    42.149831 
    8100    20622.874    253.16935            0    3690.3149   -1.0529121 
    8150    18826.468     552.8081            0    3690.5528    -26.78369 
    8200    19639.531    417.23576            0     3690.491     11.18475 
    8250     18736.82    568.57113            0    3691.3744    6.4120512 
    8300    21628.735    86.117146            0    3690.9062   -15.136564 
    8350    21300.133    140.75663            0    3690.7788   -1.3028295 
    8400     20100.75    340.28553            0    3690.4105    2.3621868 
    8450    20330.628    301.64835            0    3690.0863   -6.9035421 
    8500    21379.743    126.87873            0    3690.1693  -0.67103323 
    8550    21693.455    74.592469            0    3690.1683   -6.6175553 
    8600    20824.252    219.41263            0    3690.1212    1.7682173 
    8650    20289.679    308.59538            0    3690.2085    11.354028 
    8700    21803.688    56.071063            0    3690.0191   -2.6145414 
    8750    21111.316    171.22439            0     3689.777    6.7898851 
    8800    20775.535    227.17109            0    3689.7603    9.4162984 
    8850    19043.442    515.72721            0    3689.6343    5.3736614 
    8900    21157.163    163.34868            0    3689.5426    1.4354174 
    8950    20978.891    192.95509            0     3689.437   0.96560879 
    9000    21292.787    140.85118            0    3689.6489   -8.9387525 
    9050    20239.076     316.1505            0    3689.3299    8.0442974 
    9100    19869.892    377.60414            0    3689.2529   -7.7929877 
    9150    21454.531    113.72022            0    3689.4753   -13.322839 
    9200    17967.414    695.13611            0     3689.705    5.5120587 
    9250    20511.881    271.10991            0    3689.7567    7.4880289 
    9300    19920.611    369.49427            0    3689.5961    20.373053 
    9350    20461.102    279.43877            0    3689.6224    10.339057 
    9400    20099.827    339.51057            0    3689.4817    6.7892922 
    9450    19918.317    369.41224            0    3689.1318    10.326641 
    9500    21020.607    186.56179            0    3689.9963    7.3622937 
    9550    21179.796    160.20422            0    3690.1702   -1.0782427 
    9600    21518.982    104.08914            0    3690.5861   -5.3790399 
    9650     21206.19     156.4724            0    3690.8374    1.6109043 
    9700    21452.317     115.4785            0    3690.8646   -6.2719599 
    9750    19577.709    427.73595            0    3690.6875    -5.943044 
    9800     15600.07    1090.9222            0    3690.9338    12.384319 
    9850    18256.931    647.85044            0    3690.6723    3.3325276 
    9900    20351.693    298.44268            0    3690.3914    1.2947227 
    9950    21085.505     176.1557            0    3690.4065   -6.3748251 
   10000    18801.541    557.05356            0    3690.6438   -8.7522263 
Loop time of 3.61445 on 4 procs for 10000 steps with 81 atoms

Pair  time (%) = 0.0403561 (1.11652)
Neigh time (%) = 0.0269939 (0.746835)
Comm  time (%) = 0.19838 (5.48855)
Outpt time (%) = 0.00494462 (0.136802)
Other time (%) = 3.34377 (92.5113)

Nlocal:    20.25 ave 79 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:    46.25 ave 68 max 12 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs:    181.5 ave 722 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 726
Ave neighs/atom = 8.96296
Neighbor list builds = 990
Dangerous builds = 920
